Publications by authors named "Xuxiao Zong"

16 Publications

  • Page 1 of 1

Development and application of the Faba_bean_130K targeted next-generation sequencing SNP genotyping platform based on transcriptome sequencing.

Theor Appl Genet 2021 Jun 12. Epub 2021 Jun 12.

National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.

Key Message: Large-scale faba bean transcriptome data are available, and the first genotyping platform based on liquid-phase probe targeted capture technology was developed for genetic and molecular breeding studies. Faba bean (Vicia faba L., 2n = 12) is an important food legume crop that is widely grown for multiple uses worldwide. However, no reference genome is currently available due to its very large genome size (approximately 13 Gb) and limited single nucleotide polymorphism (SNP) markers as well as highly efficient genotyping tools have been reported for faba bean. In this study, 16.7 billion clean reads were obtained from transcriptome libraries of flowers and leaves of 102 global faba bean accessions. A total of 243,120 unigenes were de novo assembled and functionally annotated. Moreover, a total of 1,579,411 SNPs were identified and further filtered according to a selection pipeline to develop a high-throughput, flexible, low-cost Faba_bean_130K targeted next-generation sequencing (TNGS) genotyping platform. A set of 69 Chinese faba bean accessions were genotyped with the TNGS genotyping platform, and the average mapping rate of captured reads to reference transcripts was 93.14%, of which 53.23% were located in the targeted regions. The TNGS genotyping results were validated by Sanger sequencing and the average consistency rate reached 93.6%. Comprehensive population genetic analysis was performed on the 69 Chinese faba bean accessions and identified four genetic subgroups correlated with the geographic distribution. This study provides valuable genomic resources and a reliable genotyping tool that could be implemented in genetic and molecular breeding studies to accelerate new cultivar development and improvement in faba bean.
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http://dx.doi.org/10.1007/s00122-021-03885-0DOI Listing
June 2021

Genetic diversity analysis for narrow-leafed lupin (Lupinus angustifolius L.) by SSR markers.

Mol Biol Rep 2020 Jul 23;47(7):5215-5224. Epub 2020 Jun 23.

The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.

Narrow-leafed lupin (Lupinus angustifolius L.) is used as grain legumes, fodder for livestock and green manure in the world and has a great potential to be developed as a new crop in China. In this study, we assessed the genetic diversity among a set of 109 newly introduced accessions of narrow-leafed lupin using 76 genomic SSR markers. Data analysis suggested that the average gene diversity index and average polymorphism information content (PIC) were 0.4758 and 0.4328, respectively. The mean allele number per loci (Na) was 6.3816. The population structure analysis identified two subgroups based on delta K (ΔK) values. This result is in accordance with that of a PCA. The AMOVA analysis showed that most of molecular variance were within population. These results will be useful to guide the genetic improvement of the narrow-leafed lupin crop in China.
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http://dx.doi.org/10.1007/s11033-020-05596-zDOI Listing
July 2020

Two Novel Alleles Conferring Powdery Mildew () Resistance Identified in a Worldwide Collection of Pea ( L.) Germplasms.

Int J Mol Sci 2019 Oct 12;20(20). Epub 2019 Oct 12.

National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.

Powdery mildew caused by DC. severely affects pea crops worldwide. The use of resistant cultivars containing the gene is the most effective way to control this disease. The objectives of this study were to reveal alleles contained in 55 -resistant pea germplasms and to develop the functional markers of novel alleles. Sequences of 10 homologous cDNA clones from each germplasm accession were used to determine their alleles. The frame shift mutations and various alternative splicing patterns were observed during transcription of the gene. Two novel alleles, -8 and -9, were discovered in the germplasm accessions G0004839 and G0004400, respectively, and four known alleles were identified in 53 other accessions. One mutation in G0004839 was characterized by a 3-bp (GTG) deletion of the wild-type cDNA, resulting in a missing valine at position 447 of the PsMLO1 protein sequence. Another mutation in G0004400 was caused by a 1-bp (T) deletion of the wild-type cDNA sequence, resulting in a serine to leucine change of the PsMLO1 protein sequence. The -8 and -9 alleles were verified using resistance inheritance analysis and genetic mapping with respectively derived F and F populations. Finally, co-dominant functional markers specific to -8 and -9 were developed and validated in populations and pea germplasms. These results improve our understanding of resistance in pea germplasms worldwide and provide powerful tools for marker-assisted selection in pea breeding.
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http://dx.doi.org/10.3390/ijms20205071DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6829425PMC
October 2019

An RNA Sequencing Transcriptome Analysis of Grasspea ( L.) and Development of SSR and KASP Markers.

Front Plant Sci 2017 31;8:1873. Epub 2017 Oct 31.

National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.

Grasspea ( L., 2n = 14) has great agronomic potential because of its ability to survive under extreme conditions, such as drought and flood. However, this legume is less investigated because of its sparse genomic resources and very slow breeding process. In this study, 570 million quality-filtered and trimmed cDNA sequence reads with total length of over 82 billion bp were obtained using the Illumina NextSeq 500 platform. Approximately two million contigs and 142,053 transcripts were assembled from our RNA-Seq data, which resulted in 27,431 unigenes with an average length of 1,250 bp and maximum length of 48,515 bp. The unigenes were of high-quality. For example, the stay-green (SGR) gene of grasspea was aligned with the SGR gene of pea with high similarity. Among these unigenes, 3,204 EST-SSR primers were designed, 284 of which were randomly chosen for validation. Of these validated unigenes, 87 (30.6%) EST-SSR primers produced polymorphic amplicons among 43 grasspea accessions selected from different geographical locations. Meanwhile, 146,406 SNPs were screened and 50 SNP loci were randomly chosen for the kompetitive allele-specific PCR (KASP) validation. Over 80% (42) SNP loci were successfully transformed to KASP markers. Comparison of the dendrograms according to the SSR and KASP markers showed that the different marker systems are partially consistent with the dendrogram constructed in our study.
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http://dx.doi.org/10.3389/fpls.2017.01873DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5671653PMC
October 2017

Marker-trait association analysis of frost tolerance of 672 worldwide pea (Pisum sativum L.) collections.

Sci Rep 2017 07 19;7(1):5919. Epub 2017 Jul 19.

Center for Crop Germplasm Resources/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.

Frost stress is one of the major abiotic stresses causing seedling death and yield reduction in winter pea. To improve the frost tolerance of pea, field evaluation of frost tolerance was conducted on 672 diverse pea accessions at three locations in Northern China in three growing seasons from 2013 to 2016 and marker-trait association analysis of frost tolerance were performed with 267 informative SSR markers in this study. Sixteen accessions were identified as the most winter-hardy for their ability to survive in all nine field experiments with a mean survival rate of 0.57, ranging from 0.41 to 0.75. Population structure analysis revealed a structured population of two sub-populations plus some admixtures in the 672 accessions. Association analysis detected seven markers that repeatedly had associations with frost tolerance in at least two different environments with two different statistical models. One of the markers is the functional marker EST1109 on LG VI which was predicted to co-localize with a gene involved in the metabolism of glycoproteins in response to chilling stress and may provide a novel mechanism of frost tolerance in pea. These winter-hardy germplasms and frost tolerance associated markers will play a vital role in marker-assisted breeding for winter-hardy pea cultivar.
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http://dx.doi.org/10.1038/s41598-017-06222-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5517424PMC
July 2017

Soil Fertility Map for Food Legumes Production Areas in China.

Sci Rep 2016 05 23;6:26102. Epub 2016 May 23.

Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.

Given the limited resources of fossil energy, and the environmental risks of excess fertilizer on crops, it is time to reappraise the potential role of food legume biological nitrogen fixation (BNF) as sources of nitrogen for cropping systems in China. 150 soil samples across 17 provinces and 2 municipalities of China were collected and analyzed. A distribution map of the soil fertilities and their patterns of distribution was constructed. The pH results indicated that soils were neutral to slightly alkaline overall. The soil organic matter (SOM) and the available nitrogen (AN) content were relatively low, while the available phosphorus (AP) and available potassium (AK) contents were from moderate to high. Production areas of food legumes (faba bean, pea, adzuki bean, mung bean and common bean) were clearly separated into 4 soil fertility type clusters. In addition, regions with SOM, AN, AP and AK deficiency, high acidity and high alkalinity were listed as target areas for further soil improvement. The potential was considered for biological nitrogen fixation to substitute for the application of mineral nitrogen fertiliser.
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http://dx.doi.org/10.1038/srep26102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4876514PMC
May 2016

Discovery of a Novel er1 Allele Conferring Powdery Mildew Resistance in Chinese Pea (Pisum sativum L.) Landraces.

PLoS One 2016 25;11(1):e0147624. Epub 2016 Jan 25.

National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China.

Pea powdery mildew, caused by Erysiphe pisi D.C., is an important disease worldwide. Deployment of resistant varieties is the main way to control this disease. This study aimed to screen Chinese pea (Pisum sativum L.) landraces resistant to E. pisi, and to characterize the resistance gene(s) at the er1 locus in the resistant landraces, and to develop functional marker(s) specific to the novel er1 allele. The 322 landraces showed different resistance levels. Among them, 12 (3.73%), 4 (1.24%) and 17 (5.28%) landraces showed immunity, high resistance and resistance to E. pisi, respectively. The other landraces appeared susceptible or highly susceptible to E. pisi. Most of the immune and highly resistant landraces were collected from Yunnan province. To characterize the resistance gene at the er1 locus, cDNA sequences of PsMLO1 gene were determined in 12 immune and four highly resistant accessions. The cDNAs of PsMLO1 from the immune landrace G0005576 produced three distinct transcripts, characterized by a 129-bp deletion, and 155-bp and 220-bp insertions, which were consistent with those of er1-2 allele. The PsMLO1 cDNAs in the other 15 resistant landraces produced identical transcripts, which had a new point mutation (T→C) at position 1121 of PsMLO1, indicating a novel er1 allele, designated as er1-6. This mutation caused a leucine to proline change in the amino acid sequence. Subsequently, the resistance allele er1-6 in landrace G0001778 was confirmed by resistance inheritance analysis and genetic mapping on the region of the er1 locus using populations derived from G0001778 × Bawan 6. Finally, a functional marker specific to er1-6, SNP1121, was developed using the high-resolution melting technique, which could be used in pea breeding via marker-assisted selection. The results described here provide valuable genetic information for Chinese pea landraces and a powerful tool for pea breeders.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0147624PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4725671PMC
July 2016

A novel er1 allele and the development and validation of its functional marker for breeding pea (Pisum sativum L.) resistance to powdery mildew.

Theor Appl Genet 2016 May 22;129(5):909-19. Epub 2016 Jan 22.

National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, China.

Key Message: A novel er1 allele, er1 -7, conferring pea powdery mildew resistance was characterized by a 10-bp deletion in PsMLO1 cDNA, and its functional marker was developed and validated in pea germplasms. Pea powdery mildew caused by Erysiphe pisi DC is a major disease worldwide. Pea cultivar 'DDR-11' is an elite germplasm resistant to E. pisi. To identify the gene conferring resistance in DDR-11, the susceptible Bawan 6 and resistant DDR-11 cultivars were crossed to produce F1, F2, and F(2:3) populations. The phenotypic segregation patterns in the F2 and F(2:3) populations fit the 3:1 (susceptible:resistant) and 1:2:1 (susceptible homozygotes:heterozygotes:resistant homozygotes) ratios, respectively, indicating that resistance was controlled by a single recessive gene. Analysis of er1-linked markers in the F2 population suggested that the recessive resistance gene in DDR-11 was an er1 allele, which was mapped between markers ScOPE16-1600 and c5DNAmet. To further characterize er1 allele, the cDNA sequences of PsMLO1 from the parents were obtained and a novel er1 allele in DDR-11 was identified and designated as er1-7, which has a 10-bp deletion in position 111-120. The er1-7 allele caused a frame-shift mutation, resulting in a premature termination of translation of PsMLO1 protein. A co-dominant functional marker specific for er1-7 was developed, InDel111-120, which co-segregated with E. pisi resistance in the mapping population. The marker was able to distinguish between pea germplasms with and without the er1-7. Of 161 pea germplasms tested by InDel111-120, seven were detected containing resistance allele er1-7, which was verified by sequencing their PsMLO1 cDNA. Here, a novel er1 allele was characterized and its an ideal functional marker was validated, providing valuable genetic information and a powerful tool for breeding pea resistance to powdery mildew.
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http://dx.doi.org/10.1007/s00122-016-2671-9DOI Listing
May 2016

High-Throughput Development of SSR Markers from Pea (Pisum sativum L.) Based on Next Generation Sequencing of a Purified Chinese Commercial Variety.

PLoS One 2015 6;10(10):e0139775. Epub 2015 Oct 6.

The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China.

Pea (Pisum sativum L.) is an important food legume globally, and is the plant species that J.G. Mendel used to lay the foundation of modern genetics. However, genomics resources of pea are limited comparing to other crop species. Application of marker assisted selection (MAS) in pea breeding has lagged behind many other crops. Development of a large number of novel and reliable SSR (simple sequence repeat) or microsatellite markers will help both basic and applied genomics research of this crop. The Illumina HiSeq 2500 System was used to uncover 8,899 putative SSR containing sequences, and 3,275 non-redundant primers were designed to amplify these SSRs. Among the 1,644 SSRs that were randomly selected for primer validation, 841 yielded reliable amplifications of detectable polymorphisms among 24 genotypes of cultivated pea (Pisum sativum L.) and wild relatives (P. fulvum Sm.) originated from diverse geographical locations. The dataset indicated that the allele number per locus ranged from 2 to 10, and that the polymorphism information content (PIC) ranged from 0.08 to 0.82 with an average of 0.38. These 1,644 novel SSR markers were also tested for polymorphism between genotypes G0003973 and G0005527. Finally, 33 polymorphic SSR markers were anchored on the genetic linkage map of G0003973 × G0005527 F2 population.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0139775PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4595016PMC
June 2016

Genetic diversity of grasspea and its relative species revealed by SSR markers.

PLoS One 2015 20;10(3):e0118542. Epub 2015 Mar 20.

The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.

The study of genetic diversity between Lathyrus sativus L. and its relative species may yield fundamental insights into evolutionary history and provide options to meet the challenge of climate changes. 30 SSR loci were employed to assess the genetic diversity and population structure of 283 individuals from wild and domesticated populations from Africa, Europe, Asia and ICARDA. The allele number per loci ranged from 3 to 14. The average gene diversity index and average polymorphism information content (PIC) was 0.5340 and 0.4817, respectively. A model based population structure analysis divided the germplasm resources into three subgroups: the relative species, the grasspea from Asia, and the grasspea from Europe and Africa. The UPGMA dendrogram and PCA cluster also demonstrated that Asian group was convincingly separated from the other group. The AMOVA result showed that the cultivated species was quite distinct from its relative species, however a low level of differentiation was revealed among their geographic origins. In all, these results provided a molecular basis for understanding genetic diversity of L. sativus and its relatives.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0118542PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4368647PMC
December 2015

Large-scale microsatellite development in grasspea (Lathyrus sativus L.), an orphan legume of the arid areas.

BMC Plant Biol 2014 Mar 17;14:65. Epub 2014 Mar 17.

The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.

Background: Grasspea (Lathyrus sativus L., 2n = 14), a member of the family Leguminosae, holds great agronomic potential as grain and forage legume crop in the arid areas for its superb resilience to abiotic stresses such as drought, flood and salinity. The crop could not make much progress through conventional breeding in the past, and there are hardly any detailed molecular biology studies due to paucity of reliable molecular markers representative of the entire genome.

Results: Using the 454 FLX Titanium pyrosequencing technique, 651,827 simple sequence repeat (SSR) loci were identified and 50,144 nonredundant primer pairs were successfully designed, of which 288 were randomly selected for validation among 23 L. sativus and one L. cicera accessions of diverse provenance. 74 were polymorphic, 70 monomorphic, and 144 with no PCR product. The number of observed alleles ranged from two to five, the observed heterozygosity from 0 to 0.9545, and Shannon's information index ranged from 0.1013 to 1.0980, respectively. The dendrogram constructed by using unweighted pair group method with arithmetic mean (UPGMA) based on Nei's genetic distance, showed obvious distinctions and understandable relationships among the 24 accessions.

Conclusions: The large number of SSR primer pairs developed in this study would make a significant contribution to genomics enabled improvement of grasspea.
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http://dx.doi.org/10.1186/1471-2229-14-65DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4003855PMC
March 2014

Development and characterization of 20 novel polymorphic STS markers in Vicia faba (fava bean).

Am J Bot 2011 Jul 23;98(7):e189-91. Epub 2011 Jun 23.

Institute of Crop Sciences, The National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing 100081, China.

Premise Of The Study: Sequence tagged site (STS) primers were developed for Vicia faba, based on amplified bands by ISSR primers. The usefulness of these STS markers was validated for size polymorphism among fava bean accessions.

Methods And Results: Based on the sequences derived from intersimple sequence repeat (ISSR) amplification, 66 sequence tagged site (STS) primer pairs were developed and screened, and 20 of them were polymorphic. The polymorphism of these markers was identified in 32 fava bean germplasm from different global geographical locations. Alleles (N(a)) per locus numbered 2 to 4, and expected heterozygosity (H(E)) per locus ranged from 0.000 to 0.714. There was significant variation in H(E) among germplasm from different regions for individual primers.

Conclusions: These novel polymorphic STS markers may be useful and convenient for further studies of population genetics, cultivar identification, and evolution in fava bean.
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http://dx.doi.org/10.3732/ajb.1100092DOI Listing
July 2011

Development and characterization of 21 EST-derived microsatellite markers in Vicia faba (fava bean).

Am J Bot 2011 Feb 5;98(2):e22-4. Epub 2011 Jan 5.

Institute of Crop Sciences, The National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing 100081, China.

Premise Of The Study: Expressed sequence tag (EST)-derived microsatellite simple sequence repeat (SSR) markers were developed in Vicia faba L. by screening the NCBI database. Markers were validated and explored for size polymorphism among fava bean accessions.

Methods And Results: Twenty-one EST-SSR primer pairs were identified, and the loci characterized were size polymorphic among 32 fava bean genotypes from diverse geographical locations. The number of alleles (N(a)) per locus ranged from 2 to 9, and expected heterozygosity (H(E)) ranged from 0.0476 to 0.8304, respectively.

Conclusions: These markers will be useful to study genetic diversity, genetic mapping, and molecular breeding in fava bean.
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http://dx.doi.org/10.3732/ajb.1000407DOI Listing
February 2011

Molecular variation among Chinese and global winter faba bean germplasm.

Theor Appl Genet 2009 Mar 24;118(5):971-8. Epub 2009 Jan 24.

Institute of Crop Sciences/The National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 100081, Beijing, China.

A sample of winter faba bean germplasm from China was compared with germplasm from outside China, using AFLP analyses. Both sets of germplasm were obtained from the National Genebank of China, Institute of Crop Sciences (ICS), Chinese Academy of Agricultural Sciences, Beijing, China. A sample of 39 winter type accessions from outside of China and 204 Chinese landraces and varieties (201 winter types and 3 spring types) were characterized with 10 AFLP primers. These detected 266 polymorphic bands. The Chinese germplasm was clearly separated from the rest of the world in principal component analysis and clustering analysis, with the spring types from China showing the greatest separation. Yunnan germplasm, both landraces and commercial varieties, showed the greatest separation among the germplasm of Chinese winter faba bean provinces. The landraces/varieties from Anhui, Zhejiang, Sichuan, Jianxi, Guizhou and Fujian provinces clustered in a central group.
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http://dx.doi.org/10.1007/s00122-008-0954-5DOI Listing
March 2009

Analysis of a diverse global Pisum sp. collection and comparison to a Chinese local P. sativum collection with microsatellite markers.

Theor Appl Genet 2009 Jan 25;118(2):193-204. Epub 2008 Sep 25.

Institute of Crop Sciences/The National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China.

Twenty-one informative microsatellite loci were used to assess and compare the genetic diversity among Pisum genotypes sourced from within and outside China. The Chinese germplasm comprised 1243 P. sativum genotypes from 28 provinces and this was compared to 774 P. sativum genotypes that represented a globally diverse germplasm collection, as well as 103 genotypes from related Pisum species. The Chinese P. sativum germplasm was found to contain genotypes genetically distinct from the global gene pool sourced outside China. The Chinese spring type genotypes were separate from the global gene pool and from the other main Chinese gene pool of winter types. The distinct Chinese spring gene pool comprised genotypes from Inner Mongolia and Sha'anxi provinces, with those from Sha'anxi showing the greatest diversity. The other main gene pool within China included both spring types from other northern provinces and winter types from central and southern China, plus some accessions from Inner Mongolia and Sha'anxi. A core collection of Chinese landraces chosen to represent molecular diversity was compared both to the wider Chinese collection and to a geographically diverse core collection of Chinese landraces. The average gene diversity and allelic richness per locus of both the micro-satellite based core and the wider collection were similar, and greater than the geographically diverse core. The genetic diversity of P. sativum within China appears to be quite different to that detected in the global gene pool, including the presence of several rare alleles, and may be a useful source of allelic variation for both major gene and quantitative traits.
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http://dx.doi.org/10.1007/s00122-008-0887-zDOI Listing
January 2009

Low level of genetic diversity in cultivated Pigeonpea compared to its wild relatives is revealed by diversity arrays technology.

Theor Appl Genet 2006 Aug 15;113(4):585-95. Epub 2006 Jul 15.

DArT P/L, PO Box 7141, Yarralumla, ACT 2600, Australia.

Understanding the distribution of genetic diversity among individuals, populations and gene pools is crucial for the efficient management of germplasm collections and breeding programs. Diversity analysis is routinely carried out using sequencing of selected gene(s) or molecular marker technologies. Here we report on the development of Diversity Arrays Technology (DArT) for pigeonpea (Cajanus cajan) and its wild relatives. DArT tests thousands of genomic loci for polymorphism and provides the binary scores for hundreds of markers in a single hybridization-based assay. We tested eight complexity reduction methods using various combinations of restriction enzymes and selected PstI/HaeIII genomic representation with the largest frequency of polymorphic clones (19.8%) to produce genotyping arrays. The performance of the PstI/HaeIII array was evaluated by typing 96 accessions representing nearly 20 species of Cajanus. A total of nearly 700 markers were identified with the average call rate of 96.0% and the scoring reproducibility of 99.7%. DArT markers revealed genetic relationships among the accessions consistent with the available information and systematic classification. Most of the diversity was among the wild relatives of pigeonpea or between the wild species and the cultivated C. cajan. Only 64 markers were polymorphic among the cultivated accessions. Such narrow genetic base is likely to represent a serious impediment to breeding progress in pigeonpea. Our study shows that DArT can be effectively applied in molecular systematics and biodiversity studies.
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http://dx.doi.org/10.1007/s00122-006-0317-zDOI Listing
August 2006
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